# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 05:49:23 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: (2S,3S,4R,5S,6R)-5-(acetylamino)-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)[C@H](O)[C@H](O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 SAJ  SAJ  '(2S,3S,4R,5S,6R)-5-(acetylamino)-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  62  40  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SAJ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 SAJ  N1   N  NR6    0  -0.569   5.7183   0.6608  -1.7598
 SAJ  C2   C  CR6    0   0.747   6.1172   1.2634  -0.5834
 SAJ  N3   N  NR16   0  -0.733   6.5300   2.5625  -0.7143
 SAJ  C4   C  CR6    0   0.568   6.5975   3.3274  -1.8693
 SAJ  C5   C  CR16   0  -0.512   6.1578   2.6219  -3.0474
 SAJ  C6   C  CR16   0   0.103   5.7401   1.3511  -2.9392
 SAJ  O2   O  O      0  -0.468   6.1123   0.6933   0.4860
 SAJ  O4   O  O      0  -0.463   6.9956   4.4764  -1.8282
 SAJ  C1C  C  CH1    0   0.206   5.2051  -0.7031  -1.7404
 SAJ  C2C  C  CH1    0  -0.049   6.1437  -1.7793  -1.1633
 SAJ  O2C  O  OH1    0  -0.674   6.2112  -2.8275  -2.0949
 SAJ  C3C  C  CH1    0  -0.032   5.4125  -2.2401   0.1122
 SAJ  C4C  C  CH1    0   0.011   3.9577  -1.8853  -0.1881
 SAJ  O4C  O  O2     0  -0.488   4.0112  -0.7348  -1.0141
 SAJ  O3C  O  OH1    0  -0.662   5.5307  -3.6225   0.3336
 SAJ  C5C  C  CH2    0  -0.155   3.1635  -1.5889   1.0582
 SAJ  O5C  O  O2     0  -0.620   1.8131  -1.3682   0.7163
 SAJ  PA   P  P      0   1.346   0.7537  -1.1735   1.9660
 SAJ  O1A  O  O      0  -0.800   0.6189  -2.4648   2.7094
 SAJ  O2A  O  OP    -1  -0.794   1.0783   0.0939   2.6909
 SAJ  O3A  O  O2     0  -0.736  -0.5329  -0.9457   0.9705
 SAJ  PB   P  P      0   1.354  -2.0772  -1.2746   1.4309
 SAJ  O1B  O  OP    -1  -0.788  -2.4804  -2.6282   0.9415
 SAJ  O2B  O  O      0  -0.778  -2.2695  -0.8661   2.8549
 SAJ  O1'  O  O2     0  -0.635  -2.7357  -0.1249   0.4306
 SAJ  C1'  C  CH1    0   0.288  -4.0053  -0.3349  -0.1076
 SAJ  C2'  C  CH1    0  -0.184  -4.3155   0.8412  -1.0385
 SAJ  N2'  N  NH1    0  -0.627  -5.5010   0.5311  -1.8022
 SAJ  C7'  C  C      0   0.526  -5.6207   0.7288  -3.1281
 SAJ  O7'  O  O      0  -0.505  -4.7175   1.1582  -3.8317
 SAJ  C8'  C  CH3    0  -0.780  -6.9674   0.3670  -3.7054
 SAJ  C3'  C  CH1    0   0.059  -4.4775   2.1220  -0.2192
 SAJ  O3'  O  OH1    0  -0.666  -4.8443   3.1621  -1.0920
 SAJ  C4'  C  CH1    0   0.005  -5.5034   1.9114   0.8861
 SAJ  O4'  O  OH1    0  -0.709  -5.5365   3.0539   1.7018
 SAJ  C5'  C  CH1    0  -0.147  -5.1507   0.6628   1.7108
 SAJ  O5'  O  O2     0  -0.499  -4.9903  -0.4664   0.8742
 SAJ  C6'  C  C      0   0.425  -6.2431   0.3793   2.7558
 SAJ  O6A  O  OC    -1  -0.622  -6.6013   1.3966   3.4112
 SAJ  O6B  O  O      0  -0.561  -6.6731  -0.7680   2.8883
 SAJ  H1   H  HNR6   0   0.427   6.8236   3.0079   0.1467
 SAJ  H2   H  HCR6   0   0.294   6.1639   3.1188  -4.0049
 SAJ  H3   H  HCR6   0   0.330   5.3989   0.8008  -3.8044
 SAJ  H4   H  HCH1   0   0.262   5.0256  -0.9464  -2.7916
 SAJ  H5   H  HCH1   0   0.251   7.1423  -1.3832  -0.9494
 SAJ  H6   H  HOH1   0   0.448   6.1854  -3.6518  -1.5893
 SAJ  H7   H  HCH1   0   0.259   5.7716  -1.6698   0.9706
 SAJ  H8   H  HCH1   0   0.235   3.4906  -2.7190  -0.7328
 SAJ  H9   H  HOH1   0   0.470   6.2865  -3.7823   0.9075
 SAJ  H10  H  HCH2   0   0.216   3.2695  -2.4462   1.7338
 SAJ  H11  H  HCH2   0   0.213   3.5974  -0.7160   1.5606
 SAJ  H14  H  HCH1   0   0.240  -4.0377  -1.2695  -0.6771
 SAJ  H15  H  HCH1   0   0.278  -3.4930   0.9592  -1.7453
 SAJ  H16  H  HNH1   0   0.397  -6.3003   0.1706  -1.3058
 SAJ  H17  H  HCH3   0   0.266  -7.4330   1.2602  -4.1223
 SAJ  H18  H  HCH3   0   0.264  -6.8329  -0.3404  -4.5230
 SAJ  H19  H  HCH3   0   0.247  -7.6518  -0.0680  -2.9796
 SAJ  H20  H  HCH1   0   0.212  -3.5092   2.3382   0.2555
 SAJ  H21  H  HOH1   0   0.450  -4.9206   3.9681  -0.5711
 SAJ  H22  H  HCH1   0   0.186  -6.4876   1.7443   0.4133
 SAJ  H23  H  HOH1   0   0.439  -5.9904   2.7313   2.5153
 SAJ  H24  H  HCH1   0   0.237  -4.2215   0.8643   2.2615

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 SAJ  O2C  C2C  single  1.404  0.020  1.404
 SAJ  O2   C2   double  1.212  0.020  1.212
 SAJ  O3C  C3C  single  1.405  0.020  1.405
 SAJ  C2C  C3C  single  1.541  0.020  1.541
 SAJ  C2C  C1C  single  1.540  0.020  1.540
 SAJ  C2   N3   single  1.369  0.020  1.369
 SAJ  C2   N1   single  1.381  0.020  1.381
 SAJ  N3   C4   single  1.387  0.020  1.387
 SAJ  C3C  C4C  single  1.527  0.020  1.527
 SAJ  C1C  N1   single  1.457  0.020  1.457
 SAJ  C1C  O4C  single  1.398  0.020  1.398
 SAJ  N1   C6   single  1.367  0.020  1.367
 SAJ  C4   O4   double  1.217  0.020  1.217
 SAJ  C4   C5   single  1.442  0.020  1.442
 SAJ  C6   C5   double  1.342  0.020  1.342
 SAJ  O4C  C4C  single  1.417  0.020  1.417
 SAJ  C4C  C5C  single  1.507  0.020  1.507
 SAJ  O5C  C5C  single  1.410  0.020  1.410
 SAJ  O5C  PA   single  1.650  0.020  1.650
 SAJ  O1A  PA   deloc   1.496  0.020  1.496
 SAJ  PA   O3A  single  1.643  0.020  1.643
 SAJ  PA   O2A  deloc   1.496  0.020  1.496
 SAJ  O3A  PB   single  1.645  0.020  1.645
 SAJ  PB   O2B  deloc   1.494  0.020  1.494
 SAJ  PB   O1B  deloc   1.495  0.020  1.495
 SAJ  PB   O1'  single  1.660  0.020  1.660
 SAJ  O1'  C1'  single  1.395  0.020  1.395
 SAJ  C1'  C2'  single  1.532  0.020  1.532
 SAJ  C1'  O5'  single  1.397  0.020  1.397
 SAJ  C2'  N2'  single  1.444  0.020  1.444
 SAJ  C2'  C3'  single  1.529  0.020  1.529
 SAJ  O7'  C7'  double  1.223  0.020  1.223
 SAJ  O5'  C5'  single  1.414  0.020  1.414
 SAJ  C7'  N2'  single  1.346  0.020  1.346
 SAJ  C7'  C8'  single  1.509  0.020  1.509
 SAJ  C3'  O3'  single  1.406  0.020  1.406
 SAJ  C3'  C4'  single  1.523  0.020  1.523
 SAJ  C5'  C4'  single  1.537  0.020  1.537
 SAJ  C5'  C6'  single  1.538  0.020  1.538
 SAJ  C4'  O4'  single  1.404  0.020  1.404
 SAJ  O6B  C6'  deloc   1.232  0.020  1.232
 SAJ  C6'  O6A  deloc   1.262  0.020  1.262
 SAJ  N3   H1   single  0.860  0.020  1.020
 SAJ  C5   H2   single  0.930  0.020  1.080
 SAJ  C6   H3   single  0.930  0.020  1.080
 SAJ  C1C  H4   single  0.970  0.020  1.090
 SAJ  C2C  H5   single  0.970  0.020  1.090
 SAJ  O2C  H6   single  0.850  0.020  0.980
 SAJ  C3C  H7   single  0.970  0.020  1.090
 SAJ  C4C  H8   single  0.970  0.020  1.090
 SAJ  O3C  H9   single  0.850  0.020  0.980
 SAJ  C5C  H10  single  0.970  0.020  1.090
 SAJ  C5C  H11  single  0.970  0.020  1.090
 SAJ  C1'  H14  single  0.970  0.020  1.090
 SAJ  C2'  H15  single  0.970  0.020  1.090
 SAJ  N2'  H16  single  0.860  0.020  1.020
 SAJ  C8'  H17  single  0.970  0.020  1.090
 SAJ  C8'  H18  single  0.970  0.020  1.090
 SAJ  C8'  H19  single  0.970  0.020  1.090
 SAJ  C3'  H20  single  0.970  0.020  1.090
 SAJ  O3'  H21  single  0.850  0.020  0.980
 SAJ  C4'  H22  single  0.970  0.020  1.090
 SAJ  O4'  H23  single  0.850  0.020  0.980
 SAJ  C5'  H24  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 SAJ  C1C  N1   C6   119.32  3.000
 SAJ  C6   N1   C2   120.68  3.000
 SAJ  C1C  N1   C2   119.93  3.000
 SAJ  O2   C2   N3   122.13  3.000
 SAJ  N3   C2   N1   114.82  3.000
 SAJ  O2   C2   N1   123.05  3.000
 SAJ  H1   N3   C4   116.83  3.000
 SAJ  H1   N3   C2   115.04  3.000
 SAJ  C4   N3   C2   128.13  3.000
 SAJ  O4   C4   C5   126.12  3.000
 SAJ  C5   C4   N3   113.31  3.000
 SAJ  O4   C4   N3   120.57  3.000
 SAJ  H2   C5   C6   120.62  3.000
 SAJ  H2   C5   C4   119.88  3.000
 SAJ  C6   C5   C4   119.50  3.000
 SAJ  H3   C6   C5   121.06  3.000
 SAJ  H3   C6   N1   115.38  3.000
 SAJ  C5   C6   N1   123.55  3.000
 SAJ  H4   C1C  O4C  110.74  3.000
 SAJ  H4   C1C  C2C  107.74  3.000
 SAJ  O4C  C1C  C2C  108.06  3.000
 SAJ  H4   C1C  N1   104.67  3.000
 SAJ  O4C  C1C  N1   109.20  3.000
 SAJ  C2C  C1C  N1   116.38  3.000
 SAJ  H5   C2C  C3C  112.28  3.000
 SAJ  H5   C2C  O2C  110.84  3.000
 SAJ  C3C  C2C  O2C  110.42  3.000
 SAJ  H5   C2C  C1C  112.09  3.000
 SAJ  C3C  C2C  C1C  103.30  3.000
 SAJ  O2C  C2C  C1C  107.60  3.000
 SAJ  H6   O2C  C2C  106.74  3.000
 SAJ  H7   C3C  O3C  111.26  3.000
 SAJ  H7   C3C  C4C  110.28  3.000
 SAJ  O3C  C3C  C4C  109.85  3.000
 SAJ  H7   C3C  C2C  109.80  3.000
 SAJ  C4C  C3C  C2C  102.70  3.000
 SAJ  O3C  C3C  C2C  112.63  3.000
 SAJ  H8   C4C  C5C  109.56  3.000
 SAJ  H8   C4C  O4C  110.04  3.000
 SAJ  C5C  C4C  O4C  110.01  3.000
 SAJ  H8   C4C  C3C  109.02  3.000
 SAJ  C5C  C4C  C3C  112.65  3.000
 SAJ  O4C  C4C  C3C  105.50  3.000
 SAJ  C4C  O4C  C1C  110.70  3.000
 SAJ  H9   O3C  C3C  108.86  3.000
 SAJ  H11  C5C  H10  107.56  3.000
 SAJ  H11  C5C  O5C  111.42  3.000
 SAJ  H10  C5C  O5C  111.36  3.000
 SAJ  H11  C5C  C4C  109.08  3.000
 SAJ  H10  C5C  C4C  107.74  3.000
 SAJ  O5C  C5C  C4C  109.56  3.000
 SAJ  PA   O5C  C5C  116.72  3.000
 SAJ  O3A  PA   O2A  110.25  3.000
 SAJ  O2A  PA   O1A  120.67  3.000
 SAJ  O3A  PA   O1A  110.50  3.000
 SAJ  O2A  PA   O5C  109.13  3.000
 SAJ  O3A  PA   O5C   93.45  3.000
 SAJ  O1A  PA   O5C  109.42  3.000
 SAJ  PB   O3A  PA   122.55  3.000
 SAJ  O1'  PB   O2B  109.51  3.000
 SAJ  O1'  PB   O1B  108.83  3.000
 SAJ  O2B  PB   O1B  121.67  3.000
 SAJ  O1'  PB   O3A   93.74  3.000
 SAJ  O1B  PB   O3A  110.04  3.000
 SAJ  O2B  PB   O3A  109.45  3.000
 SAJ  C1'  O1'  PB   119.29  3.000
 SAJ  H14  C1'  O5'  105.33  3.000
 SAJ  H14  C1'  C2'  109.48  3.000
 SAJ  O5'  C1'  C2'  110.90  3.000
 SAJ  H14  C1'  O1'  110.86  3.000
 SAJ  O5'  C1'  O1'  112.63  3.000
 SAJ  C2'  C1'  O1'  107.65  3.000
 SAJ  H15  C2'  C3'  109.66  3.000
 SAJ  H15  C2'  N2'  107.43  3.000
 SAJ  C3'  C2'  N2'  112.10  3.000
 SAJ  H15  C2'  C1'  108.91  3.000
 SAJ  C3'  C2'  C1'  109.82  3.000
 SAJ  N2'  C2'  C1'  108.83  3.000
 SAJ  H16  N2'  C7'  117.87  3.000
 SAJ  H16  N2'  C2'  117.87  3.000
 SAJ  C7'  N2'  C2'  124.23  3.000
 SAJ  C8'  C7'  O7'  121.54  3.000
 SAJ  C8'  C7'  N2'  114.90  3.000
 SAJ  O7'  C7'  N2'  123.56  3.000
 SAJ  H19  C8'  H18  108.58  3.000
 SAJ  H19  C8'  H17  108.30  3.000
 SAJ  H18  C8'  H17  107.33  3.000
 SAJ  H19  C8'  C7'  113.69  3.000
 SAJ  H18  C8'  C7'  109.42  3.000
 SAJ  H17  C8'  C7'  109.32  3.000
 SAJ  H20  C3'  C4'  107.88  3.000
 SAJ  H20  C3'  O3'  110.61  3.000
 SAJ  C4'  C3'  O3'  112.15  3.000
 SAJ  H20  C3'  C2'  107.62  3.000
 SAJ  C4'  C3'  C2'  110.15  3.000
 SAJ  O3'  C3'  C2'  108.34  3.000
 SAJ  H21  O3'  C3'  107.70  3.000
 SAJ  H22  C4'  C5'  108.13  3.000
 SAJ  H22  C4'  O4'  110.54  3.000
 SAJ  C5'  C4'  O4'  110.77  3.000
 SAJ  H22  C4'  C3'  108.10  3.000
 SAJ  O4'  C4'  C3'  108.97  3.000
 SAJ  C5'  C4'  C3'  110.31  3.000
 SAJ  H23  O4'  C4'  102.94  3.000
 SAJ  H24  C5'  C6'  107.09  3.000
 SAJ  H24  C5'  O5'  110.30  3.000
 SAJ  C6'  C5'  O5'  109.59  3.000
 SAJ  H24  C5'  C4'  108.30  3.000
 SAJ  C6'  C5'  C4'  110.56  3.000
 SAJ  O5'  C5'  C4'  110.93  3.000
 SAJ  C5'  O5'  C1'  114.87  3.000
 SAJ  O6B  C6'  O6A  126.55  3.000
 SAJ  O6A  C6'  C5'  113.94  3.000
 SAJ  O6B  C6'  C5'  119.50  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 SAJ  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 SAJ  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 SAJ  CONST_03  C1C  N1   C2   N3   180.00   0.0  0
 SAJ  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 SAJ  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 SAJ  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 SAJ  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 SAJ  CONST_08  C1C  N1   C2   O2     0.00   0.0  0
 SAJ  CONST_09  H1   N3   C2   N1   180.00   0.0  0
 SAJ  CONST_10  O7'  C7'  N2'  C2'    0.00   0.0  0
 SAJ  CONST_11  C8'  C7'  N2'  C2'  180.00   0.0  0
 SAJ  CONST_12  H16  N2'  C7'  O7'  180.00   0.0  0
 SAJ  Var_01    O1A  PA   O5C  C5C  -67.77  30.0  3
 SAJ  Var_02    O2B  PB   O3A  PA    38.95  30.0  3
 SAJ  Var_03    H10  C5C  O5C  PA    55.08  30.0  3
 SAJ  Var_04    H17  C8'  C7'  N2'  117.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SAJ  chir_01  C1C  C2C  N1   O4C  positiv
 SAJ  chir_02  C2C  O2C  C3C  C1C  positiv
 SAJ  chir_03  C3C  O3C  C4C  C2C  positiv
 SAJ  chir_04  C4C  O4C  C3C  C5C  negativ
 SAJ  chir_07  C1'  O1'  C2'  O5'  positiv
 SAJ  chir_08  C2'  N2'  C3'  C1'  negativ
 SAJ  chir_09  C3'  O3'  C2'  C4'  positiv
 SAJ  chir_10  C4'  O4'  C3'  C5'  negativ
 SAJ  chir_11  C5'  O5'  C4'  C6'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SAJ  plan-1  N1   0.020
 SAJ  plan-1  C2   0.020
 SAJ  plan-1  N3   0.020
 SAJ  plan-1  C4   0.020
 SAJ  plan-1  C5   0.020
 SAJ  plan-1  C6   0.020
 SAJ  plan-1  O2   0.020
 SAJ  plan-1  O4   0.020
 SAJ  plan-1  C1C  0.020
 SAJ  plan-1  H1   0.020
 SAJ  plan-1  H2   0.020
 SAJ  plan-1  H3   0.020
 SAJ  plan-2  C2'  0.020
 SAJ  plan-2  N2'  0.020
 SAJ  plan-2  C7'  0.020
 SAJ  plan-2  O7'  0.020
 SAJ  plan-2  C8'  0.020
 SAJ  plan-2  H16  0.020
 SAJ  plan-3  C5'  0.020
 SAJ  plan-3  C6'  0.020
 SAJ  plan-3  O6A  0.020
 SAJ  plan-3  O6B  0.020

